Spanish media said the two leaders had "decided to co-ordinate" their response to next year's referendum in Scotland and continuing calls for secession in Catalonia.
The development came after Spanish Prime Minister Mariano Rajoy asserted an independent Scotland would be "left outside the EU" and required to negotiate membership from scratch with all 28 member states.
The claims of a deal between the two men were dismissed by Downing Street last night, although sources confirmed Mr Cameron and Mr Rajoy had discussed the independence issue while attending a summit of EU leaders.
An article in the Spanish newspaper El Pais said the two had "agreed the necessity to explain to citizens the consequences secession would have" - namely, independence for Scotland or Catalonia would result in their "automatic expulsion from the EU".
"It is very important the public be told the truth," said Mr Rajoy.
First Minister Alex Salmond claims an independent Scotland would be fast-tracked into the EU and the Scottish Government has published a document expanding on its case for bypassing the usual, often protracted, EU accession procedures..
A No 10 source said David Cameron and Mr Rajoy had spoken in the margins of the summit yesterday. "Mr Rajoy repeated what he had said on an independent Scotland's EU membership. The PM noted what he said. That was it." He added: "We don't recognise talk of a deal."
A spokeswoman for Deputy First Minister Nicola Sturgeon said: "Mr Rajoy has previously indicated he considers the Scottish and Catalan situations are 'absolutely and totally different'.
"Scotland is already an integral part of the EU and there is nothing in the entire body of EU treaties which provides for the expulsion of an existing territory or the removal of its inhabitants' rights as EU citizens."